One goal of the Section on Drosophila Gene Regulation is to understand the regulation of homeotic gene function in Drosophila. The homeotic genes encode homeodomain-containing transcription factors that control cell fates by regulating the transcription of downstream target genes. The homeotic genes are expressed in precise spatial patterns that are crucial for the proper determination of segmental identities. The homeotic genes themselves, as well as the trans-acting factors that regulate their expression, are conserved between Drosophila and human. Understanding the regulation and function of the homeotic genes is crucial to understanding human development. Cis-acting transcriptional regulatory elements from the homeotic genes have been previously-identified by assays in transgenes in Drosophila. These assays have identified both tissue-specific enhancer elements, as well as cis-regulatory elements that are required for the maintenance of activation or repression throughout development. While these transgene assays have been important in defining the structure of the cis-regulatory elements and identifying trans-acting factors that bind them, their functions within the contexts of the endogenous genes is still not well understood. Using a transgene assay, we have identified five candidate fragments of DNA from the Sex combs reduced gene that cause transcriptional silencing of a reporter gene. These cis-regulatory silencing elements require the trans-acting proteins encoded by the Polycomb group genes. We have deleted three of these cis-regulatory silencing elements within the endogenous Sex combs reduced gene, with no discernible effects on silencing. We have also simultaneously deleted all three cis-regulatory silencing elements within the Sex combs reduced gene, again with no discernible effects on silencing. Genetic studies first identified the Polycomb group genes by their defects in transcriptional silencing of the homeotic genes. To identify new Polycomb group genes, we have developed a transgene assay using the cis-regulatory silencing elements from the Sex combs reduced homeotic gene. Recessive mutations that disrupt transgene silencing are recovered in mitotic clones in heterozygous flies. We have screened about 98% of the genome and isolated over 340 mutants that disrupt Polycomb-dependent silencing. About one-third of these mutants are not mutations in genes that disrupt silencing, but are chromosome aberrations that generate aneuploid cells following mitotic recombination. Transgene silencing is disrupted in these cells due to changes in copy numbers of the transgene. The remaining two thirds of the mutants disrupt Polycomb-dependent silencing because they carry mutations in genes required to maintain Polycomb-dependent silencing. We have mapped 228 mutations to 63 complementation groups required for Polycomb-dependent silencing, including almost all of the known Polycomb group genes. The transcription units for 46 of the 63 genes have been identified, and encode DNA-binding proteins, chromatin-remodelling factors, histone-modifying enzymes, transcription factors, kinases, phosphatases, and two amino-acyl tRNA synthetases. Genetic defects that cause male infertility are common in both man and Drosophila. We have shown that mutations to male sterility in Drosophila are about 15% as common as mutations to lethality, suggesting that a substantial proportion of the Drosophila genome may be required only for male fertility. As expected from these results, we have also found that as much as 20-25% of the Drosophila proteome may be expressed only in males. The proportions of genes required for male fertility do not differ significantly between the X chromosome and the autosomes, however, translocations that exchange large portions of the X chromosome and one of the two large autosomes frequently disrupt spermatogenesis. We have generated a set of new X-autosomal translocations and are using them to test a model of differential transcriptional regulation that was proposed fifty years ago to explain this phenomenon.